Well I tried to use a few mods which was available on this site which are: C&C, TAWD and XTA99. They do not have any ta3d.mod or info.mod in the archive so I had to create these on my own. when I put those mods in .ta3d/mods and starting TA3D they are not shown at all but when I put those mods in .ta3d/resources/mods instead TA3D shows these available mods but it does not properly load it and it just loads regular TA stuff.

ta3d.log doesn't mention any of these mods when it is loaded, also I am using Linux Mint 18 and the TA3D version is 0.6.0 I tried both the compiled version and the repository none of these loaded the mods properly.

I put the CNC mod in ~/.ta3d/resources/mods/cnc and it has info.mod there too, so when I start up the game it will let me select TA:World Domination and the C&C mod but as soon one of those mod is loaded it shows on skirmish menu only the 2 default faction names ARM and CORE so it wont even let me select the new faction and in-game there is no differences either so it looks the same as if only the default mod got loaded.

That's interesting, in both files the names of the 2 sides are ARM and CORE and since it is where TA3D looks for these names it's what it shows. What happens if you select ARM or CORE and start a game ?